diff --git a/regtest/dimred/rt-mds/analysis.0.embed.reference b/regtest/dimred/rt-mds/analysis.0.embed.reference
index bfcd2c1e88ce54595c66627548ecfb3cf83829c6..3ebfef2be81d00feef14247ece1453aaf9d7259d 100644
--- a/regtest/dimred/rt-mds/analysis.0.embed.reference
+++ b/regtest/dimred/rt-mds/analysis.0.embed.reference
@@ -1,698 +1,698 @@
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=650626174834469268094976.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0873 mds.2=0.0013
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7551 c1.moment-3=1.3322
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=3443064697932843889721344.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0535 mds.2=0.0044
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7434 c1.moment-3=1.3003
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=4334990767809816147525632.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0150 mds.2=0.0044
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7333 c1.moment-3=1.2632
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1642551053927491148185600.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0136 mds.2=0.0019
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7283 c1.moment-3=1.2349
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=565077236443374117978112.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0308 mds.2=-0.0012
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7268 c1.moment-3=1.2175
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=506902826865531421720576.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0355 mds.2=-0.0018
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7262 c1.moment-3=1.2128
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=3497441683667193365004288.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0090 mds.2=-0.0015
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7327 c1.moment-3=1.2385
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=5816989471131786348068864.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0145 mds.2=0.0004
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7371 c1.moment-3=1.2616
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=5197629206541778607407104.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0191 mds.2=0.0022
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7366 c1.moment-3=1.2666
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=22568578815140474208124928.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0278 mds.2=0.0015
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7394 c1.moment-3=1.2748
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=8891751619370481308663808.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0091 mds.2=-0.0004
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7365 c1.moment-3=1.2562
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=145469732262582499147776.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0359 mds.2=-0.0012
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7255 c1.moment-3=1.2126
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=67243488566443176361984.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0540 mds.2=0.0004
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7193 c1.moment-3=1.1955
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=991674944473569693794304.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0322 mds.2=-0.0034
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7286 c1.moment-3=1.2156
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=433704577708501378269184.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0205 mds.2=-0.0150
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7429 c1.moment-3=1.2239
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=58924815689464923815936.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0282 mds.2=-0.0289
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7542 c1.moment-3=1.2128
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=28876419368888716754944.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0530 mds.2=-0.0358
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7544 c1.moment-3=1.1871
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=29493206461009996283904.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0769 mds.2=-0.0312
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7438 c1.moment-3=1.1652
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=15523379316519734345728.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0893 mds.2=-0.0259
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7355 c1.moment-3=1.1546
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=6036949107489532542976.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0697 mds.2=-0.0246
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7393 c1.moment-3=1.1739
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=6805982676529049501696.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
-REMARK mds.1=-0.0301 mds.2=-0.0196
+REMARK mds.1=-0.0302 mds.2=-0.0196
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7448 c1.moment-3=1.2133
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=224283114659648425164800.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0093 mds.2=-0.0072
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7430 c1.moment-3=1.2547
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1937631236154971427700736.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0274 mds.2=0.0009
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7400 c1.moment-3=1.2742
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=8943884514170369755578368.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0301 mds.2=0.0016
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7400 c1.moment-3=1.2770
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1818542782073875176882176.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0265 mds.2=-0.0033
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7438 c1.moment-3=1.2723
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=356284804122361993363456.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0433 mds.2=-0.0053
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7501 c1.moment-3=1.2879
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=740928158795493248335872.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0514 mds.2=-0.0019
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7489 c1.moment-3=1.2967
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=3971376819483128291655680.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0222 mds.2=0.0031
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7365 c1.moment-3=1.2698
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=3616045831357711704391680.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0129 mds.2=0.0061
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7245 c1.moment-3=1.2366
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=866118050097568367509504.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0322 mds.2=0.0084
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7172 c1.moment-3=1.2186
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=473876430918082860417024.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0355 mds.2=0.0080
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7168 c1.moment-3=1.2153
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=549108949631639043964928.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0337 mds.2=0.0067
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7185 c1.moment-3=1.2168
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=714866179522068016529408.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0308 mds.2=0.0047
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7211 c1.moment-3=1.2191
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1514315762407424940572672.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0253 mds.2=0.0016
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7255 c1.moment-3=1.2235
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1741401785128748918505472.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0132 mds.2=-0.0021
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7323 c1.moment-3=1.2343
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=3707685932716769910194176.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0040 mds.2=-0.0031
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7377 c1.moment-3=1.2506
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=5279612145243834875379712.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0107 mds.2=0.0011
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7354 c1.moment-3=1.2582
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=14648991633879816569094144.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0299 mds.2=0.0060
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7357 c1.moment-3=1.2780
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=101745406227893881592086528.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0540 mds.2=0.0070
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7410 c1.moment-3=1.3015
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=77977698769596315733065728.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0650 mds.2=0.0039
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7468 c1.moment-3=1.3114
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=5438198764112726743580672.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0415 mds.2=0.0025
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7421 c1.moment-3=1.2882
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1122421932113435130068992.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0074 mds.2=0.0033
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7325 c1.moment-3=1.2555
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1623375579255821794541568.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0185 mds.2=0.0059
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7232 c1.moment-3=1.2312
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=824284132438079344476160.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0413 mds.2=0.0073
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7158 c1.moment-3=1.2096
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=418023780265421327826944.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0548 mds.2=0.0074
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7123 c1.moment-3=1.1966
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=524201540254286764572672.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0385 mds.2=0.0041
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7197 c1.moment-3=1.2114
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=255645304728742904463360.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0383 mds.2=-0.0006
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7243 c1.moment-3=1.2104
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=80831060875928311693312.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0584 mds.2=-0.0008
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7192 c1.moment-3=1.1910
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=410072896508362208837632.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0584 mds.2=0.0023
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7162 c1.moment-3=1.1918
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=473315368593257205334016.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0553 mds.2=0.0090
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7105 c1.moment-3=1.1965
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=49342818148888732499968.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0772 mds.2=0.0146
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6995 c1.moment-3=1.1768
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=71439214621479799881728.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0757 mds.2=0.0157
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6988 c1.moment-3=1.1785
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=372382770456105985245184.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0644 mds.2=0.0144
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7030 c1.moment-3=1.1891
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=396750501333421147553792.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0816 mds.2=0.0141
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6988 c1.moment-3=1.1724
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=194367523462455551328256.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.1045 mds.2=0.0148
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6922 c1.moment-3=1.1504
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=265390023546441746612224.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0867 mds.2=0.0111
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7004 c1.moment-3=1.1667
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=417842650383208029356032.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0365 mds.2=0.0014
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7228 c1.moment-3=1.2126
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=130034479906962406375424.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0113 mds.2=-0.0067
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7431 c1.moment-3=1.2567
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=453748863537616517070848.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0272 mds.2=-0.0074
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7479 c1.moment-3=1.2718
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=2549987501327281773608960.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0381 mds.2=-0.0012
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7448 c1.moment-3=1.2840
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=3357671899518696282914816.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0548 mds.2=0.0021
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7459 c1.moment-3=1.3010
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=2973694890310422329556992.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0470 mds.2=0.0012
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7447 c1.moment-3=1.2933
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=288602953154320790454272.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0227 mds.2=-0.0019
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7414 c1.moment-3=1.2690
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1760887739729704734687232.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0132 mds.2=-0.0022
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7392 c1.moment-3=1.2597
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1526973208100442807992320.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0040 mds.2=0.0004
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7343 c1.moment-3=1.2515
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=375263178685270183641088.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0045 mds.2=0.0008
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7317 c1.moment-3=1.2434
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=232661556808622295482368.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0145 mds.2=0.0006
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7293 c1.moment-3=1.2337
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=507064184978749788258304.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0116 mds.2=0.0025
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7282 c1.moment-3=1.2370
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1128952088522002253479936.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0031 mds.2=0.0044
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7286 c1.moment-3=1.2457
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1197960641606570746052608.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0148 mds.2=0.0086
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7216 c1.moment-3=1.2355
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=625774095016588059082752.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0318 mds.2=0.0109
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7149 c1.moment-3=1.2196
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=364912544013506169536512.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0166 mds.2=0.0078
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7218 c1.moment-3=1.2336
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1649391353916835862937600.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0154 mds.2=0.0036
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7342 c1.moment-3=1.2633
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=11346816644974575838298112.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0451 mds.2=0.0018
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7437 c1.moment-3=1.2915
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=20791509453694539808112640.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0364 mds.2=0.0021
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7411 c1.moment-3=1.2832
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1867515982473692874539008.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0125 mds.2=0.0036
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7335 c1.moment-3=1.2606
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=11344083134102028704284672.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0330 mds.2=0.0045
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7379 c1.moment-3=1.2806
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=120911330589421810499977216.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0605 mds.2=0.0048
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7448 c1.moment-3=1.3072
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=40351160276202809800523776.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0417 mds.2=0.0041
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7406 c1.moment-3=1.2889
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=9235968903630373689229312.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0115 mds.2=0.0011
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7356 c1.moment-3=1.2590
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=15198595282354971818852352.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0257 mds.2=-0.0018
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7421 c1.moment-3=1.2719
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=14695620601365390340128768.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0451 mds.2=-0.0029
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7483 c1.moment-3=1.2904
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=3504618985646781185916928.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0387 mds.2=-0.0032
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7469 c1.moment-3=1.2841
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1958037545372794977517568.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0254 mds.2=-0.0017
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7420 c1.moment-3=1.2716
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=7729740074168141073088512.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0311 mds.2=-0.0001
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7418 c1.moment-3=1.2775
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=26429041345273132897796096.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0448 mds.2=0.0006
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7448 c1.moment-3=1.2909
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=37403428414373558822633472.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0499 mds.2=0.0020
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7448 c1.moment-3=1.2962
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=69071824065210548899282944.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0543 mds.2=0.0037
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7443 c1.moment-3=1.3009
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=28746486049325375245254656.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0486 mds.2=0.0054
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7412 c1.moment-3=1.2959
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=5138199027537960106983424.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0459 mds.2=0.0051
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7407 c1.moment-3=1.2932
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=20730130763570579884736512.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0715 mds.2=-0.0001
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7524 c1.moment-3=1.3166
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=10053248420830524810985472.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0764 mds.2=-0.0063
REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7596 c1.moment-3=1.3196
+REMARK c1.moment-2=0.7597 c1.moment-3=1.3196
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=2341097486254890020765696.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0603 mds.2=-0.0119
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7609 c1.moment-3=1.3027
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1801241546807460694589440.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0378 mds.2=-0.0153
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7583 c1.moment-3=1.2800
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=2623886374903733202976768.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0214 mds.2=-0.0124
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7512 c1.moment-3=1.2649
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1540127025264497029808128.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0063 mds.2=-0.0091
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7441 c1.moment-3=1.2513
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=761250478060893041065984.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0095 mds.2=-0.0016
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7327 c1.moment-3=1.2380
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=815550859201229044580352.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0259 mds.2=0.0036
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7234 c1.moment-3=1.2235
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=1031052805964853080489984.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0234 mds.2=0.0061
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7217 c1.moment-3=1.2265
END
DESCRIPTION: analysis data from calculation done at time 5.000000
-REMARK WEIGHT=828970472636431535702016.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0012 mds.2=0.0060
REMARK ARG=c1.moment-2,c1.moment-3
diff --git a/regtest/dimred/rt-mds/analysis.0.list_embed.reference b/regtest/dimred/rt-mds/analysis.0.list_embed.reference
index ce29c25f6a5ecf50ae070443c00face1089a9d06..185b19ed5558aa853b2fd67022b2c0c1250983a2 100644
--- a/regtest/dimred/rt-mds/analysis.0.list_embed.reference
+++ b/regtest/dimred/rt-mds/analysis.0.list_embed.reference
@@ -19,7 +19,7 @@
-0.0769 -0.0312
-0.0893 -0.0259
-0.0697 -0.0246
- -0.0301 -0.0196
+ -0.0302 -0.0196
0.0093 -0.0072
0.0274 0.0009
0.0301 0.0016
diff --git a/regtest/dimred/rt-mds/embed.reference b/regtest/dimred/rt-mds/embed.reference
index 8ecbcfdae735a3b83db48ea0b5db1d88179d9a6f..336cec6f8141b43fd3bbf4c0f9d630e6cf3550ad 100644
--- a/regtest/dimred/rt-mds/embed.reference
+++ b/regtest/dimred/rt-mds/embed.reference
@@ -1,698 +1,698 @@
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0008
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0594 mds.2=0.0053
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7340 c1.moment-3=1.2672
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0012
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0683 mds.2=0.0034
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7371 c1.moment-3=1.2758
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0004
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0705 mds.2=0.0006
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7401 c1.moment-3=1.2777
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0010
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0729 mds.2=-0.0019
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7428 c1.moment-3=1.2796
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0022
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0874 mds.2=-0.0069
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7497 c1.moment-3=1.2934
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0019
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0961 mds.2=-0.0095
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7533 c1.moment-3=1.3018
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0023
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0867 mds.2=-0.0062
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7489 c1.moment-3=1.2928
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0030
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0719 mds.2=-0.0008
REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7417 c1.moment-3=1.2788
+REMARK c1.moment-2=0.7417 c1.moment-3=1.2789
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0118
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0575 mds.2=0.0031
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7360 c1.moment-3=1.2651
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0063
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0552 mds.2=0.0034
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7354 c1.moment-3=1.2628
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0022
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0682 mds.2=-0.0002
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7405 c1.moment-3=1.2753
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0029
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0781 mds.2=-0.0024
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7440 c1.moment-3=1.2847
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0010
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0785 mds.2=-0.0025
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7441 c1.moment-3=1.2852
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0004
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0763 mds.2=-0.0027
REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7441 c1.moment-3=1.2829
+REMARK c1.moment-2=0.7441 c1.moment-3=1.2830
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0013
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0755 mds.2=-0.0041
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7454 c1.moment-3=1.2820
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0069
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0792 mds.2=-0.0069
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7486 c1.moment-3=1.2853
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0096
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0778 mds.2=-0.0062
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7477 c1.moment-3=1.2840
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0076
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0727 mds.2=-0.0025
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7434 c1.moment-3=1.2795
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0143
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0726 mds.2=0.0014
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7396 c1.moment-3=1.2798
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0302
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0756 mds.2=0.0030
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7384 c1.moment-3=1.2830
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0171
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0821 mds.2=0.0017
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7405 c1.moment-3=1.2893
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0013
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0816 mds.2=0.0001
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7420 c1.moment-3=1.2886
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0167
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0774 mds.2=0.0008
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7407 c1.moment-3=1.2845
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0234
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0766 mds.2=0.0008
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7407 c1.moment-3=1.2837
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0171
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0838 mds.2=-0.0005
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7429 c1.moment-3=1.2906
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0265
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0931 mds.2=-0.0016
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7452 c1.moment-3=1.2997
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0521
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0936 mds.2=-0.0010
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7446 c1.moment-3=1.3004
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0504
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0923 mds.2=-0.0009
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7443 c1.moment-3=1.2990
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0443
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0906 mds.2=-0.0008
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7440 c1.moment-3=1.2974
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0270
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0706 mds.2=0.0025
REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7382 c1.moment-3=1.2780
+REMARK c1.moment-2=0.7382 c1.moment-3=1.2779
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0120
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0664 mds.2=0.0050
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7352 c1.moment-3=1.2741
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0517
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0901 mds.2=0.0019
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7412 c1.moment-3=1.2972
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0821
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.1059 mds.2=-0.0015
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7467 c1.moment-3=1.3125
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0206
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0917 mds.2=0.0006
REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7428 c1.moment-3=1.2986
+REMARK c1.moment-2=0.7428 c1.moment-3=1.2987
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0206
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0876 mds.2=0.0021
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7407 c1.moment-3=1.2948
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0207
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.1008 mds.2=-0.0001
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7446 c1.moment-3=1.3076
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0270
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0955 mds.2=-0.0014
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7452 c1.moment-3=1.3022
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0171
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0858 mds.2=-0.0018
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7444 c1.moment-3=1.2925
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0345
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0894 mds.2=-0.0005
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7436 c1.moment-3=1.2963
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0819
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0922 mds.2=0.0014
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7420 c1.moment-3=1.2992
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.1159
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0917 mds.2=0.0010
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7423 c1.moment-3=1.2987
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0266
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0925 mds.2=-0.0043
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7477 c1.moment-3=1.2989
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0072
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0967 mds.2=-0.0102
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7541 c1.moment-3=1.3023
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0358
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.1073 mds.2=-0.0096
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7548 c1.moment-3=1.3129
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0264
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.1065 mds.2=-0.0047
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7499 c1.moment-3=1.3126
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0087
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0935 mds.2=-0.0003
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7439 c1.moment-3=1.3003
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0055
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0668 mds.2=0.0049
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7353 c1.moment-3=1.2745
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0047
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
-REMARK mds.1=0.0411 mds.2=0.0087
+REMARK mds.1=0.0410 mds.2=0.0086
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7284 c1.moment-3=1.2494
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0049
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0264 mds.2=0.0110
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7242 c1.moment-3=1.2352
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0014
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0254 mds.2=0.0125
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7226 c1.moment-3=1.2344
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0015
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0503 mds.2=0.0085
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7297 c1.moment-3=1.2586
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0025
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0855 mds.2=0.0007
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7419 c1.moment-3=1.2925
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0045
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0975 mds.2=-0.0028
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7469 c1.moment-3=1.3039
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0336
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0983 mds.2=-0.0035
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7477 c1.moment-3=1.3047
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0570
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0997 mds.2=-0.0044
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7487 c1.moment-3=1.3059
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0021
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0877 mds.2=-0.0021
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7449 c1.moment-3=1.2944
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0002
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0501 mds.2=0.0053
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7328 c1.moment-3=1.2580
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0004
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0104 mds.2=0.0140
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7192 c1.moment-3=1.2197
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0009
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0199 mds.2=0.0221
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7074 c1.moment-3=1.1907
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0004
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0416 mds.2=0.0277
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6990 c1.moment-3=1.1698
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0688 mds.2=0.0338
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6895 c1.moment-3=1.1436
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0858 mds.2=0.0354
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6858 c1.moment-3=1.1269
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0897 mds.2=0.0313
REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6894 c1.moment-3=1.1226
+REMARK c1.moment-2=0.6894 c1.moment-3=1.1225
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0920 mds.2=0.0254
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6950 c1.moment-3=1.1195
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.1168 mds.2=0.0227
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6945 c1.moment-3=1.0946
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0001
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.1447 mds.2=0.0227
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6910 c1.moment-3=1.0669
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0004
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.1636 mds.2=0.0221
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6892 c1.moment-3=1.0481
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0011
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.1461 mds.2=0.0182
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6953 c1.moment-3=1.0650
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0004
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.1212 mds.2=0.0139
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7027 c1.moment-3=1.0891
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0005
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0775 mds.2=0.0056
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7164 c1.moment-3=1.1314
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0004
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0008 mds.2=-0.0041
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7358 c1.moment-3=1.2063
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0007
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0469 mds.2=-0.0038
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7415 c1.moment-3=1.2537
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0074
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0771 mds.2=-0.0004
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7419 c1.moment-3=1.2840
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0384
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0917 mds.2=0.0005
REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7428 c1.moment-3=1.2986
+REMARK c1.moment-2=0.7428 c1.moment-3=1.2987
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0153
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0656 mds.2=0.0042
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7359 c1.moment-3=1.2732
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0016
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0034 mds.2=0.0115
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7200 c1.moment-3=1.2057
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0006
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0901 mds.2=0.0141
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7064 c1.moment-3=1.1200
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0005
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.1784 mds.2=0.0069
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7024 c1.moment-3=1.0315
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0002
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.2253 mds.2=-0.0077
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7109 c1.moment-3=0.9832
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0001
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.2372 mds.2=-0.0248
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7264 c1.moment-3=0.9692
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.2415 mds.2=-0.0448
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7456 c1.moment-3=0.9624
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.2562 mds.2=-0.0539
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7529 c1.moment-3=0.9466
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.2901 mds.2=-0.0433
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7381 c1.moment-3=0.9144
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.3173 mds.2=-0.0215
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7130 c1.moment-3=0.8902
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.3117 mds.2=0.0096
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6829 c1.moment-3=0.8996
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.2787 mds.2=0.0317
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6651 c1.moment-3=0.9352
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.2319 mds.2=0.0372
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.6656 c1.moment-3=0.9823
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.1897 mds.2=0.0305
REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6776 c1.moment-3=1.0233
+REMARK c1.moment-2=0.6775 c1.moment-3=1.0233
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0001
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.1592 mds.2=0.0142
REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6975 c1.moment-3=1.0515
+REMARK c1.moment-2=0.6975 c1.moment-3=1.0514
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
-REMARK mds.1=-0.1211 mds.2=-0.0049
+REMARK mds.1=-0.1212 mds.2=-0.0049
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7213 c1.moment-3=1.0868
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0960 mds.2=-0.0150
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7345 c1.moment-3=1.1105
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0001
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0842 mds.2=-0.0162
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7372 c1.moment-3=1.1221
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0001
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0813 mds.2=-0.0187
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7401 c1.moment-3=1.1246
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0823 mds.2=-0.0193
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7406 c1.moment-3=1.1235
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0773 mds.2=-0.0179
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7398 c1.moment-3=1.1287
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0621 mds.2=-0.0202
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7440 c1.moment-3=1.1435
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0449 mds.2=-0.0215
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7475 c1.moment-3=1.1604
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0269 mds.2=-0.0307
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7589 c1.moment-3=1.1770
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0000
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=-0.0075 mds.2=-0.0368
REMARK ARG=c1.moment-2,c1.moment-3
REMARK c1.moment-2=0.7673 c1.moment-3=1.1955
END
DESCRIPTION: analysis data from calculation done at time 10.000000
-REMARK WEIGHT=0.0002
+REMARK WEIGHT=1.0000
REMARK PROPERTIES=mds.1,mds.2
REMARK mds.1=0.0266 mds.2=-0.0342
REMARK ARG=c1.moment-2,c1.moment-3
diff --git a/regtest/dimred/rt-mds/list_embed.reference b/regtest/dimred/rt-mds/list_embed.reference
index 2f4fb6096a9baef0d55b0c24a64cc504a1b9021a..b24c465dfceac9021d1e5b3dec7800870f408522 100644
--- a/regtest/dimred/rt-mds/list_embed.reference
+++ b/regtest/dimred/rt-mds/list_embed.reference
@@ -46,7 +46,7 @@
0.1065 -0.0047
0.0935 -0.0003
0.0668 0.0049
- 0.0411 0.0087
+ 0.0410 0.0086
0.0264 0.0110
0.0254 0.0125
0.0503 0.0085
@@ -88,7 +88,7 @@
-0.2319 0.0372
-0.1897 0.0305
-0.1592 0.0142
- -0.1211 -0.0049
+ -0.1212 -0.0049
-0.0960 -0.0150
-0.0842 -0.0162
-0.0813 -0.0187
diff --git a/regtest/dimred/rt-mds/plumed.dat b/regtest/dimred/rt-mds/plumed.dat
index 1c63ced777d2fdf193f3b62edd3ccae373a17bd9..e74a9549425442c105389e8ab42cd2f853d02273 100755
--- a/regtest/dimred/rt-mds/plumed.dat
+++ b/regtest/dimred/rt-mds/plumed.dat
@@ -17,7 +17,7 @@ UPPER_WALLS ARG=d7 AT=2.0 KAPPA=100.
COORDINATIONNUMBER SPECIES=1-7 MOMENTS=2-3 SWITCH={RATIONAL R_0=1.5 NN=8 MM=16} LABEL=c1
-oo: EUCLIDEAN_DISSIMILARITIES ARG=c1.moment-2,c1.moment-3 STRIDE=10 RUN=1000 REWEIGHT_TEMP=0.1 TEMP=0.2
+oo: EUCLIDEAN_DISSIMILARITIES ARG=c1.moment-2,c1.moment-3 STRIDE=10 RUN=1000
CLASSICAL_MDS ...
USE_OUTPUT_DATA_FROM=oo
diff --git a/src/analysis/AnalysisBase.h b/src/analysis/AnalysisBase.h
index 2717ce3873b9b40a189d31367f997ba9e3bb319e..7893e9782f788422f5b6e9af7af06c9227c18639 100644
--- a/src/analysis/AnalysisBase.h
+++ b/src/analysis/AnalysisBase.h
@@ -82,7 +82,7 @@ public:
/// Get the ith data point
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
- virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, bool& isprojection );
+ virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
/// Get the input configuration (in dimensionality reduction this returns the high dimensional configuration)
virtual ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// This actually performs the analysis
@@ -159,8 +159,8 @@ void AnalysisBase::getDataPoint( const unsigned& idata, std::vector<double>& poi
}
inline
-ReferenceConfiguration* AnalysisBase::getReferenceConfiguration( const unsigned& idata, bool& isprojection ){
- return mydata->getReferenceConfiguration( idata, isprojection );
+ReferenceConfiguration* AnalysisBase::getReferenceConfiguration( const unsigned& idata ){
+ return mydata->getReferenceConfiguration( idata );
}
inline
diff --git a/src/analysis/AnalysisWithDataCollection.cpp b/src/analysis/AnalysisWithDataCollection.cpp
index 61ddf9edde9f69406c4841ed6dd0324f64f81d56..1d3586edca0cb492294a2a2219eb75a838517fd2 100644
--- a/src/analysis/AnalysisWithDataCollection.cpp
+++ b/src/analysis/AnalysisWithDataCollection.cpp
@@ -36,7 +36,10 @@ void AnalysisWithDataCollection::registerKeywords( Keywords& keys ){
AnalysisBase::registerKeywords( keys );
keys.use("ARG"); keys.reset_style("ARG","atoms-1");
keys.add("atoms-1","ATOMS","the atoms whose positions we are tracking for the purpose of analysing the data");
- keys.add("hidden","METRIC","how are we measuring the distances between configurations. If you have only arguments this will by default be the euclidean metric. You must specify a metric if you are analysing atoms");
+ keys.add("hidden","METRIC","how are we measuring the distances between configurations. If you have only arguments this will by default be the euclidean "
+ "metric. You must specify a metric if you are analysing atoms. You can choose any of the metrics described in the part of the "
+ "manual on \\ref dists. If your metric involves multiple different blocks of atoms then you can use repeated ATOMS keywords "
+ "i.e. ATOMS1, ATOMS2 etc. You can also add additional information on your metric in this command.");
keys.add("atoms-1","STRIDE","the frequency with which data should be stored for analysis. By default data is collected on every step");
keys.add("atoms-1","RUN","the frequency with which to run the analysis algorithms.");
keys.addFlag("USE_ALL_DATA",false,"just analyse all the data in the trajectory. This option should be used in tandem with ATOMS/ARG + STRIDE");
@@ -75,21 +78,38 @@ old_norm(0.0)
// we must collect data from the trajectory
} else {
// Get information on numbers of atoms and argument names
- std::vector<AtomNumber> atom_numbers; std::vector<std::string> argument_names( getNumberOfArguments() );
+ std::vector<std::string> argument_names( getNumberOfArguments() );
for(unsigned i=0;i<getNumberOfArguments();++i) argument_names[i]=getPntrToArgument(i)->getName();
-
+ if( getNumberOfArguments()>0 ) mypdb.addArgumentNames( argument_names );
// Read in information on the metric that is being used in this analysis object
- parse("METRIC",metricname);
- if( metricname.length()==0 ) metricname="EUCLIDEAN";
+ std::string metrictmp; parse("METRIC",metrictmp);
+ if( metrictmp.length()==0 ){
+ metricname="EUCLIDEAN";
+ } else {
+ std::vector<std::string> metricwords = Tools::getWords( metrictmp );
+ metricname=metricwords[0]; metricwords.erase(metricwords.begin());
+ mypdb.addRemark( metricwords );
+ }
ReferenceConfiguration* checkref=metricRegister().create<ReferenceConfiguration>( metricname );
// Check if we should read atoms
ReferenceAtoms* hasatoms=dynamic_cast<ReferenceAtoms*>( checkref );
if( hasatoms ){
- parseAtomList("ATOMS",atom_numbers); requestAtoms(atom_numbers);
- if( atom_numbers.size()==0 ) error("no atom positions have been specified in input");
- log.printf(" monitoring positions of atoms ");
- for(unsigned i=0;i<atom_numbers.size();++i) log.printf("%d ",atom_numbers[i].serial() );
- log.printf("\n");
+ std::vector<AtomNumber> atom_numbers; parseAtomList("ATOMS",atom_numbers);
+ if( atom_numbers.size()>0 ){
+ log.printf(" monitoring positions of atoms ");
+ for(unsigned i=0;i<atom_numbers.size();++i) log.printf("%d ",atom_numbers[i].serial() );
+ log.printf("\n"); mypdb.addBlockEnd( atom_numbers.size() );
+ } else {
+ std::vector<AtomNumber> tmpatoms; mypdb.addBlockEnd(0);
+ for(unsigned i=1;;++i){
+ parseAtomList("ATOMS",i,tmpatoms);
+ if( i==1 && tmpatoms.size()==0 ) error("no atom positions have been specified in input");
+ else if( tmpatoms.size()==0 ) break;
+ for(unsigned j=0;j<tmpatoms.size();++j) atom_numbers.push_back( tmpatoms[j] );
+ mypdb.addBlockEnd( atom_numbers.size() );
+ }
+ }
+ requestAtoms(atom_numbers); mypdb.setAtomNumbers( atom_numbers );
}
// Check if we should read arguments
ReferenceArguments* hasargs=dynamic_cast<ReferenceArguments*>( checkref );
@@ -107,10 +127,7 @@ old_norm(0.0)
// Setup everything given the ammount of data that we will have in each analysis
if( freq%getStride()!= 0 ) error("Frequncy of running is not a multiple of the stride");
unsigned ndata=freq/getStride(); data.resize(ndata); logweights.resize( ndata );
- for(unsigned i=0;i<ndata;++i){
- data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
- data[i]->setNamesAndAtomNumbers( atom_numbers, argument_names );
- }
+ for(unsigned i=0;i<ndata;++i) data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
log.printf(" running analysis every %u steps\n",freq);
// Check if we are doing block averaging
parseFlag("NOMEMORY",nomemory);
@@ -189,10 +206,10 @@ void AnalysisWithDataCollection::readCheckPointFile( const std::string& filename
if(fp!=NULL){
bool do_read=true, first=true;
while (do_read) {
- PDB mypdb;
- do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
+ PDB tpdb;
+ do_read=tpdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
if(do_read){
- data[idata]->set( mypdb );
+ data[idata]->set( tpdb );
data[idata]->parse("TIME",tstep);
if( !first && ((tstep-oldtstep) - getStride()*plumed.getAtoms().getTimeStep())>plumed.getAtoms().getTimeStep() ){
error("frequency of data storage in " + filename + " is not equal to frequency of data storage plumed.dat file");
@@ -229,9 +246,9 @@ void AnalysisWithDataCollection::getDataPoint( const unsigned& idat, std::vector
}
}
-ReferenceConfiguration* AnalysisWithDataCollection::getReferenceConfiguration( const unsigned& idat, bool& isprojection ){
- if( !mydata ){ plumed_dbg_assert( idat<data.size() ); isprojection=false; return data[idat]; }
- return AnalysisBase::getReferenceConfiguration( idat, isprojection );
+ReferenceConfiguration* AnalysisWithDataCollection::getReferenceConfiguration( const unsigned& idat ){
+ if( !mydata ){ plumed_dbg_assert( idat<data.size() ); return data[idat]; }
+ return AnalysisBase::getReferenceConfiguration( idat );
}
ReferenceConfiguration* AnalysisWithDataCollection::getInputReferenceConfiguration( const unsigned& idat ){
@@ -259,24 +276,22 @@ void AnalysisWithDataCollection::update(){
// Reweighting because of biases
if( !biases.empty() ) ww += bias/simtemp;
- // Get the arguments ready to transfer to reference configuration
- std::vector<double> current_args( getNumberOfArguments() );
- for(unsigned i=0;i<getNumberOfArguments();++i) current_args[i]=getArgument(i);
- // Could add stuff for fancy metrics here eventually but for now unecessary
- std::vector<double> mymetric( getNumberOfArguments(), 1.0 );
-
+ // Pass the atom positions to the pdb
+ mypdb.setAtomPositions( getPositions() );
+ // Pass the argument values to the pdb
+ for(unsigned i=0;i<getNumberOfArguments();++i){
+ mypdb.setArgumentValue( getPntrToArgument(i)->getName(), getArgument(i) );
+ }
+ // Could add stuff for mahalanobis distance etc here eventually but for now unecessary
+
if(use_all_data){
data.push_back( metricRegister().create<ReferenceConfiguration>( metricname ) );
plumed_dbg_assert( data.size()==idata+1 );
- std::vector<std::string> argument_names( getNumberOfArguments() );
- for(unsigned i=0;i<getNumberOfArguments();++i) argument_names[i] = getPntrToArgument(i)->getName();
- data[idata]->setNamesAndAtomNumbers( getAbsoluteIndexes(), argument_names );
- data[idata]->setReferenceConfig( getPositions(), current_args, mymetric );
- logweights.push_back(ww);
+ data[idata]->set( mypdb ); logweights.push_back(ww);
} else {
// Get the arguments and store them in a vector of vectors
- data[idata]->setReferenceConfig( getPositions(), current_args, mymetric );
- logweights[idata] = ww;
+ // We have to clear all properties from previous analyses prior to setting the data
+ data[idata]->clearAllProperties(); data[idata]->set( mypdb ); logweights[idata] = ww;
}
// Write data to checkpoint file
diff --git a/src/analysis/AnalysisWithDataCollection.h b/src/analysis/AnalysisWithDataCollection.h
index 2a54464dbf873c7d0cd2102d1891c330f96da783..97ec59d8eceafc916a77b028a01fbef7b0dc61a0 100644
--- a/src/analysis/AnalysisWithDataCollection.h
+++ b/src/analysis/AnalysisWithDataCollection.h
@@ -23,6 +23,7 @@
#define __PLUMED_analysis_AnalysisWithDataCollection_h
#include "AnalysisBase.h"
+#include "tools/PDB.h"
namespace PLMD {
@@ -52,8 +53,9 @@ private:
bool firstAnalysisDone;
/// The value of the old normalization constant
double norm, old_norm;
-/// List of argument names
- std::vector<std::string> argument_names;
+/// Data is collected from the trajectory by passing it to this pdb. These pdb
+/// files are then read by the ReferenceConfigurations in data
+ PDB mypdb;
/// The type of metric we are using to measure distances
std::string metricname;
/// The checkpoint file --- really I would like to get rid of this and have some universal mechanism and a single file GT
@@ -88,7 +90,7 @@ public:
/// Get the ith data point
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
- virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat, bool& isprojection );
+ virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
/// Get the underlying reference configuration (in dimensionality reduction this return the high dimensional point)
ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idat );
/// This ensures that the energy is stored if we are reweighting
diff --git a/src/analysis/EuclideanDissimilarityMatrix.cpp b/src/analysis/EuclideanDissimilarityMatrix.cpp
index 2e5cd733ea95e460260ebf4911726bb0b28a2c61..d8d8ac5686ae8072d1404e4f1bc2c5f223bed72a 100644
--- a/src/analysis/EuclideanDissimilarityMatrix.cpp
+++ b/src/analysis/EuclideanDissimilarityMatrix.cpp
@@ -73,8 +73,7 @@ double EuclideanDissimilarityMatrix::getDissimilarity( const unsigned& iframe, c
plumed_dbg_assert( iframe<dissimilarities.nrows() && jframe<dissimilarities.ncols() );
if( dissimilarities(iframe,jframe)>0. ){ return dissimilarities(iframe,jframe); }
if( iframe!=jframe ){
- bool ignore;
- dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = distance( getPbc(), getArguments(), getReferenceConfiguration(iframe,ignore), getReferenceConfiguration(jframe,ignore), true );
+ dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = distance( getPbc(), getArguments(), getReferenceConfiguration(iframe), getReferenceConfiguration(jframe), true );
return dissimilarities(iframe,jframe);
}
return 0.0;
diff --git a/src/analysis/LandmarkSelectionBase.h b/src/analysis/LandmarkSelectionBase.h
index 5a91ffe6f8d839c7be60e21e7f96684827aebb31..09d56554559db50f199d2da098adc0d08ec6fce6 100644
--- a/src/analysis/LandmarkSelectionBase.h
+++ b/src/analysis/LandmarkSelectionBase.h
@@ -54,7 +54,7 @@ public:
/// Get the ith data point
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat, bool& isprojection );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
/// Select landmark configurations
void performAnalysis();
virtual void selectLandmarks()=0;
@@ -85,8 +85,8 @@ void LandmarkSelectionBase::getDataPoint( const unsigned& idata, std::vector<dou
}
inline
-ReferenceConfiguration* LandmarkSelectionBase::getReferenceConfiguration( const unsigned& idat, bool& isprojection ){
- return AnalysisWithDataCollection::getReferenceConfiguration( landmark_indices[idat], isprojection );
+ReferenceConfiguration* LandmarkSelectionBase::getReferenceConfiguration( const unsigned& idat ){
+ return AnalysisWithDataCollection::getReferenceConfiguration( landmark_indices[idat] );
}
inline
diff --git a/src/analysis/OutputColvarFile.cpp b/src/analysis/OutputColvarFile.cpp
index df589e265c6860421a66c3aa5818379c5907120a..fe56fc3d0b20934ec52e2194a8d4273ff113a365 100644
--- a/src/analysis/OutputColvarFile.cpp
+++ b/src/analysis/OutputColvarFile.cpp
@@ -88,17 +88,21 @@ void OutputColvarFile::performAnalysis(){
gfile.fmtField(fmt+" ");
gfile.open( filename.c_str() );
- // Can't print out all landmark data if we have reference atom positions
- bool ignore;
- ReferenceAtoms* myat=dynamic_cast<ReferenceAtoms*>( getReferenceConfiguration(0,ignore) );
- plumed_assert( !myat );
-
+ ReferenceConfiguration* myp = getReferenceConfiguration(0);
+ if( myp->getNumberOfProperties()==0 ) plumed_assert( !dynamic_cast<ReferenceAtoms*>( myp ) );
+
// Print embedding coordinates
for(unsigned i=0;i<getNumberOfDataPoints();++i){
- ReferenceArguments* myref=dynamic_cast<ReferenceArguments*>( getReferenceConfiguration(i,ignore) );
- plumed_assert( myref );
- for(unsigned j=0;j<myref->getReferenceArguments().size();++j){
- gfile.printField( myref->getArgumentNames()[j], myref->getReferenceArgument(j) );
+ ReferenceConfiguration* mypoint=getReferenceConfiguration(i);
+ for(unsigned j=0;j<mypoint->getNumberOfProperties();++j){
+ gfile.printField( mypoint->getPropertyName(j), mypoint->getPropertyValue(j) );
+ }
+ if( mypoint->getNumberOfProperties()==0 ){
+ ReferenceArguments* myref=dynamic_cast<ReferenceArguments*>( mypoint );
+ plumed_assert( myref );
+ for(unsigned j=0;j<myref->getReferenceArguments().size();++j){
+ gfile.printField( myref->getArgumentNames()[j], myref->getReferenceArgument(j) );
+ }
}
gfile.printField();
}
diff --git a/src/analysis/OutputPDBFile.cpp b/src/analysis/OutputPDBFile.cpp
index 6112115e16f11d5f54af7e603d253383683d22b3..ae0fa1db6793b72013851a0b3249f737e03357dd 100644
--- a/src/analysis/OutputPDBFile.cpp
+++ b/src/analysis/OutputPDBFile.cpp
@@ -77,18 +77,12 @@ fmt("%f")
void OutputPDBFile::performAnalysis(){
// Output the embedding in plumed pdb format
OFile afile; afile.link(*this); afile.setBackupString("analysis"); std::size_t psign=fmt.find("%");
- afile.open( filename.c_str() ); bool isprojection; std::string descr="REMARK WEIGHT=%-" + fmt.substr(psign+1) + "\n";
+ afile.open( filename.c_str() ); std::string descr="REMARK WEIGHT=%-" + fmt.substr(psign+1) + "\n";
for(unsigned j=0;j<getNumberOfDataPoints();++j){
afile.printf("DESCRIPTION: analysis data from calculation done at time %f \n",getLabel().c_str(),getTime() );
afile.printf(descr.c_str(),getWeight(j) );
- ReferenceConfiguration* myref = getReferenceConfiguration(j,isprojection);
- if( plumed.getAtoms().usingNaturalUnits() ) myref->print( 1.0, afile, fmt, isprojection );
- else myref->print( plumed.getAtoms().getUnits().getLength()/0.1, afile, fmt, isprojection );
- // This ensures the high dimensional position is projected if we are working with dimensionality reduction
- if( isprojection ){
- if( plumed.getAtoms().usingNaturalUnits() ) getInputReferenceConfiguration(j)->print( 1.0, afile, fmt, false );
- else getInputReferenceConfiguration(j)->print( plumed.getAtoms().getUnits().getLength()/0.1, afile, fmt, false );
- }
+ if( plumed.getAtoms().usingNaturalUnits() ) getReferenceConfiguration(j)->print( 1.0, afile, fmt );
+ else getReferenceConfiguration(j)->print( plumed.getAtoms().getUnits().getLength()/0.1, afile, fmt );
}
afile.close();
}
diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp
index 03df61abb5905804a54926028568ef06309d7b37..7dec6c1ddd1171dcadd447d32f52569fd9c6a0e2 100644
--- a/src/analysis/ReadDissimilarityMatrix.cpp
+++ b/src/analysis/ReadDissimilarityMatrix.cpp
@@ -48,7 +48,7 @@ public:
ReadDissimilarityMatrix( const ActionOptions& ao );
unsigned getNumberOfDataPoints() const { return nnodes; }
/// This gives an error as if we read in the matrix we dont have the coordinates
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, bool& isprojection );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// This gives an error as if we read in the matrix we dont have the coordinates
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
@@ -124,7 +124,7 @@ double ReadDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const
return dissimilarities( iframe, jframe );
}
-ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( const unsigned& idata, bool& isprojection ){
+ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( const unsigned& idata ){
plumed_merror("cannot get reference configurations from read in dissimilarity matrix");
return NULL;
}
diff --git a/src/dimred/DimensionalityReductionBase.cpp b/src/dimred/DimensionalityReductionBase.cpp
index 505bbe4bb8ebdb37118803e1aa4b422527461580..364695734a7cebf3ec5f5d4e6fb38b6b7307b7fe 100644
--- a/src/dimred/DimensionalityReductionBase.cpp
+++ b/src/dimred/DimensionalityReductionBase.cpp
@@ -21,7 +21,6 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "DimensionalityReductionBase.h"
#include "reference/ReferenceConfiguration.h"
-#include "reference/MetricRegister.h"
#include "core/PlumedMain.h"
#include "core/Atoms.h"
@@ -36,7 +35,6 @@ void DimensionalityReductionBase::registerKeywords( Keywords& keys ){
DimensionalityReductionBase::DimensionalityReductionBase( const ActionOptions& ao ):
Action(ao),
analysis::AnalysisBase(ao),
-myref(NULL),
dimredbase(NULL)
{
// Check that some dissimilarity information is available
@@ -52,23 +50,12 @@ dimredbase(NULL)
if( nlow<1 ) error("dimensionality of low dimensional space must be at least one");
}
log.printf(" projecting in %d dimensional space \n",nlow);
-
- ReferenceConfigurationOptions("EUCLIDEAN");
- myref=metricRegister().create<ReferenceConfiguration>("EUCLIDEAN");
- std::vector<std::string> dimnames(nlow); std::string num;
- for(unsigned i=0;i<nlow;++i){ Tools::convert(i+1,num); dimnames[i] = getLabel() + "." + num; }
- myref->setNamesAndAtomNumbers( std::vector<AtomNumber>(), dimnames );
-}
-
-DimensionalityReductionBase::~DimensionalityReductionBase(){
- delete myref;
}
-ReferenceConfiguration* DimensionalityReductionBase::getReferenceConfiguration( const unsigned& idat, bool& isprojection ){
- std::vector<double> pp(nlow); for(unsigned i=0;i<nlow;++i) pp[i]=projections(idat,i);
- std::vector<double> empty( pp.size() ); isprojection=true;
- myref->setReferenceConfig( std::vector<Vector>(), pp, empty );
- return myref;
+ReferenceConfiguration* DimensionalityReductionBase::getReferenceConfiguration( const unsigned& idat ){
+ ReferenceConfiguration* myref = mydata->getInputReferenceConfiguration( idat ); std::string num; myref->clearAllProperties();
+ for(unsigned i=0;i<nlow;++i){ Tools::convert(i+1,num); myref->attachProperty( getLabel() + "." + num, projections(idat,i) ); }
+ return myref;
}
ReferenceConfiguration* DimensionalityReductionBase::getInputReferenceConfiguration( const unsigned& idat ){
diff --git a/src/dimred/DimensionalityReductionBase.h b/src/dimred/DimensionalityReductionBase.h
index 66725aa8036123d3b9ac5cd5d73f8b0a928ebcb7..e06be9d81980fd5259983f8106bb5692c1a4bb85 100644
--- a/src/dimred/DimensionalityReductionBase.h
+++ b/src/dimred/DimensionalityReductionBase.h
@@ -34,9 +34,6 @@ private:
/// This are the target distances for a single point.
/// This is used when we do out of sample or pointwise global optimization
std::vector<double> dtargets;
-/// We create a reference configuration here so that we can pass projection data
-/// quickly
- ReferenceConfiguration* myref;
/// The projections that were generated by the dimensionality reduction algorithm
Matrix<double> projections;
protected:
@@ -47,11 +44,10 @@ protected:
public:
static void registerKeywords( Keywords& keys );
DimensionalityReductionBase( const ActionOptions& );
- ~DimensionalityReductionBase();
/// Get the ith data point (this returns the projection)
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (this returns the projection)
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, bool& isprojection );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// Actually perform the analysis
void performAnalysis();
diff --git a/src/dimred/ProjectNonLandmarkPoints.cpp b/src/dimred/ProjectNonLandmarkPoints.cpp
index a606ffb315722dab216a8edf5254120f631bb32d..0dc28f101bbca8c99dcd5045108fdb2c9e898381 100644
--- a/src/dimred/ProjectNonLandmarkPoints.cpp
+++ b/src/dimred/ProjectNonLandmarkPoints.cpp
@@ -23,9 +23,9 @@
#include "core/PlumedMain.h"
#include "core/ActionSet.h"
#include "tools/Random.h"
-#include "reference/MetricRegister.h"
#include "tools/ConjugateGradient.h"
#include "analysis/AnalysisBase.h"
+#include "reference/ReferenceConfiguration.h"
#include "DimensionalityReductionBase.h"
//+PLUMEDOC DIMRED PROJECT_ALL_ANALYSIS_DATA
@@ -46,22 +46,18 @@ private:
double cgtol;
/// Number of diemsions in low dimensional space
unsigned nlow;
-/// We create a reference configuration here so that we can pass projection data
-/// quickly
- ReferenceConfiguration* myref;
/// The class that calcualtes the projection of the data that is required
DimensionalityReductionBase* mybase;
/// Generate a projection of the ith data point - this is called in two routine
- void generateProjection( const unsigned& idata, std::vector<double>& point );
+ void generateProjection( const unsigned& idat, std::vector<double>& point );
public:
static void registerKeywords( Keywords& keys );
ProjectNonLandmarkPoints( const ActionOptions& ao );
- ~ProjectNonLandmarkPoints();
/// Get the ith data point (this returns the projection)
- void getDataPoint( const unsigned& idata, std::vector<double>& point );
+ void getDataPoint( const unsigned& idat, std::vector<double>& point );
/// Get a reference configuration (this returns the projection)
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, bool& isprojection );
- ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
+ ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idat );
/// This does nothing -- projections are calculated when getDataPoint and getReferenceConfiguration are called
void performAnalysis(){}
/// This just calls calculate stress in the underlying projection object
@@ -92,24 +88,14 @@ mybase(NULL)
log.printf(" generating out-of-sample projections using projection with label %s \n",myproj.c_str() );
parse("CGTOL",cgtol);
-
- ReferenceConfigurationOptions("EUCLIDEAN");
- myref=metricRegister().create<ReferenceConfiguration>("EUCLIDEAN");
- std::vector<std::string> dimnames(nlow); std::string num;
- for(unsigned i=0;i<nlow;++i){ Tools::convert(i+1,num); dimnames[i] = getLabel() + "." + num; }
- myref->setNamesAndAtomNumbers( std::vector<AtomNumber>(), dimnames );
-}
-
-ProjectNonLandmarkPoints::~ProjectNonLandmarkPoints(){
- delete myref;
}
-void ProjectNonLandmarkPoints::generateProjection( const unsigned& idata, std::vector<double>& point ){
+void ProjectNonLandmarkPoints::generateProjection( const unsigned& idat, std::vector<double>& point ){
ConjugateGradient<ProjectNonLandmarkPoints> myminimiser( this );
- unsigned closest=0; double mindist = sqrt( getDissimilarity( idata, mybase->getDataPointIndexInBase(0) ) );
+ unsigned closest=0; double mindist = sqrt( getDissimilarity( idat, mybase->getDataPointIndexInBase(0) ) );
mybase->setTargetDistance( 0, mindist );
for(unsigned i=1;i<mybase->getNumberOfDataPoints();++i){
- double dist = sqrt( getDissimilarity( idata, mybase->getDataPointIndexInBase(i) ) );
+ double dist = sqrt( getDissimilarity( idat, mybase->getDataPointIndexInBase(i) ) );
mybase->setTargetDistance( i, dist );
if( dist<mindist ){ mindist=dist; closest=i; }
}
@@ -119,19 +105,20 @@ void ProjectNonLandmarkPoints::generateProjection( const unsigned& idata, std::v
myminimiser.minimise( cgtol, point, &ProjectNonLandmarkPoints::calculateStress );
}
-ReferenceConfiguration* ProjectNonLandmarkPoints::getReferenceConfiguration( const unsigned& idata, bool& isprojection ){
- std::vector<double> pp(nlow); std::vector<double> empty( pp.size() ); generateProjection( idata, pp );
- myref->setReferenceConfig( std::vector<Vector>(), pp, empty ); isprojection=true;
+ReferenceConfiguration* ProjectNonLandmarkPoints::getReferenceConfiguration( const unsigned& idat ){
+ std::vector<double> pp(nlow); generateProjection( idat, pp ); std::string num;
+ ReferenceConfiguration* myref = mydata->getInputReferenceConfiguration( idat ); myref->clearAllProperties();
+ for(unsigned i=0;i<nlow;++i){ Tools::convert(i+1,num); myref->attachProperty( getLabel() + "." + num, pp[i] ); }
return myref;
}
-ReferenceConfiguration* ProjectNonLandmarkPoints::getInputReferenceConfiguration( const unsigned& idata ){
- return mydata->getInputReferenceConfiguration( idata );
+ReferenceConfiguration* ProjectNonLandmarkPoints::getInputReferenceConfiguration( const unsigned& idat ){
+ return mydata->getInputReferenceConfiguration( idat );
}
-void ProjectNonLandmarkPoints::getDataPoint( const unsigned& idata, std::vector<double>& point ){
+void ProjectNonLandmarkPoints::getDataPoint( const unsigned& idat, std::vector<double>& point ){
if( point.size()!=nlow ) point.resize( nlow );
- generateProjection( idata, point );
+ generateProjection( idat, point );
}
double ProjectNonLandmarkPoints::calculateStress( const std::vector<double>& pp, std::vector<double>& der ){
diff --git a/src/mapping/Mapping.cpp b/src/mapping/Mapping.cpp
index b3ba5d58df84d0c3e2fbeb8bd68498bf17a2a3a6..2a8fcaed3cac5c4c68d41871048e2f9eb59beb99 100644
--- a/src/mapping/Mapping.cpp
+++ b/src/mapping/Mapping.cpp
@@ -106,9 +106,9 @@ ActionWithVessel(ao)
requestAtoms( atoms ); std::vector<Value*> req_args;
interpretArgumentList( args, req_args ); requestArguments( req_args );
// Duplicate all frames (duplicates are used by sketch-map)
- mymap->duplicateFrameList();
+ // mymap->duplicateFrameList();
// fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
- plumed_assert( !mymap->mappingNeedsSetup() );
+ // plumed_assert( !mymap->mappingNeedsSetup() );
// Resize all derivative arrays
// mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
// Resize forces array
@@ -128,25 +128,25 @@ Mapping::~Mapping(){
delete mymap;
}
-void Mapping::prepare(){
- if( mymap->mappingNeedsSetup() ){
- // Get the arguments and atoms that are required
- std::vector<AtomNumber> atoms; std::vector<std::string> args;
- mymap->getAtomAndArgumentRequirements( atoms, args );
- requestAtoms( atoms ); std::vector<Value*> req_args;
- interpretArgumentList( args, req_args ); requestArguments( req_args );
- // Duplicate all frames (duplicates are used by sketch-map)
- mymap->duplicateFrameList();
- // Get the number of frames in the path
- unsigned nfram=getNumberOfReferencePoints();
- // fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
- plumed_assert( !mymap->mappingNeedsSetup() );
- // Resize all derivative arrays
- // mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
- // Resize forces array
- forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
- }
-}
+// void Mapping::prepare(){
+// if( mymap->mappingNeedsSetup() ){
+// // Get the arguments and atoms that are required
+// std::vector<AtomNumber> atoms; std::vector<std::string> args;
+// mymap->getAtomAndArgumentRequirements( atoms, args );
+// requestAtoms( atoms ); std::vector<Value*> req_args;
+// interpretArgumentList( args, req_args ); requestArguments( req_args );
+// // Duplicate all frames (duplicates are used by sketch-map)
+// // mymap->duplicateFrameList();
+// // Get the number of frames in the path
+// unsigned nfram=getNumberOfReferencePoints();
+// // fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
+// plumed_assert( !mymap->mappingNeedsSetup() );
+// // Resize all derivative arrays
+// // mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
+// // Resize forces array
+// forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
+// }
+// }
unsigned Mapping::getPropertyIndex( const std::string& name ) const {
return mymap->getPropertyIndex( name );
diff --git a/src/mapping/Mapping.h b/src/mapping/Mapping.h
index 855f91576493e33c257dc8eb3b67b2d9d335b5b3..4fb4ea05631cebd7744f5796675a17344a1d8833 100644
--- a/src/mapping/Mapping.h
+++ b/src/mapping/Mapping.h
@@ -91,7 +91,7 @@ public:
/// Get the value of the ith property for the current frame
double getPropertyValue( const unsigned& current, const unsigned& iprop ) const ;
/// Stuff to do before we do the calculation
- void prepare();
+// void prepare();
/// Apply the forces
void apply();
};
diff --git a/src/mapping/PCAVars.cpp b/src/mapping/PCAVars.cpp
index aaf1ad0d183b6047fcbbd45b4a2721749885ca4c..928b1fbf63619c3f373f7a283ce4814a8cd28db0 100644
--- a/src/mapping/PCAVars.cpp
+++ b/src/mapping/PCAVars.cpp
@@ -274,8 +274,6 @@ mypack(0,0,myvals)
/// This sets up all the storage data required by PCA in the pack
myframes.getFrame(0)->setupPCAStorage( mypack );
- // Retrieve the position of the first frame, as we use this for alignment
- myref->setNamesAndAtomNumbers( atoms, args );
// Check there are no periodic arguments
for(unsigned i=0;i<getNumberOfArguments();++i){
if( getPntrToArgument(i)->isPeriodic() ) error("cannot use periodic variables in pca projections");
diff --git a/src/reference/MultiDomainRMSD.cpp b/src/reference/MultiDomainRMSD.cpp
index c87317502ea3e1365489ea21f9a42a09915683d6..b9e1eca5b911ab57e05df2740a2bbaaa674cfd28 100644
--- a/src/reference/MultiDomainRMSD.cpp
+++ b/src/reference/MultiDomainRMSD.cpp
@@ -79,7 +79,8 @@ void MultiDomainRMSD::read( const PDB& pdb ){
else weights.push_back( ww );
}
// And set the atom numbers for this object
- setAtomNumbers( pdb.getAtomNumbers() );
+ for(unsigned i=0;i<pdb.size();++i){ indices.push_back( pdb.getAtomNumbers()[i] ); der_index.push_back(i); }
+ // setAtomNumbers( pdb.getAtomNumbers() );
}
void MultiDomainRMSD::setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in ){
diff --git a/src/reference/MultiReferenceBase.cpp b/src/reference/MultiReferenceBase.cpp
index fcfdd2337ccee5e687be1c70190e3cd3d0f35940..cd2ed45d0724d5483250281488bb7e3e8465b9b7 100644
--- a/src/reference/MultiReferenceBase.cpp
+++ b/src/reference/MultiReferenceBase.cpp
@@ -70,20 +70,20 @@ void MultiReferenceBase::getAtomAndArgumentRequirements( std::vector<AtomNumber>
// }
// }
-void MultiReferenceBase::copyFrame( ReferenceConfiguration* frameToCopy ){
- // Create a reference configuration of the appropriate type
- ReferenceConfiguration* mymsd=metricRegister().create<ReferenceConfiguration>( frameToCopy->getName() );
- // Copy names of arguments and and indexes
- mymsd->setNamesAndAtomNumbers( frameToCopy->getAbsoluteIndexes(), frameToCopy->getArgumentNames() );
- // Copy reference positions, reference arguments and reference metric
- mymsd->setReferenceConfig( frameToCopy->getReferencePositions(), frameToCopy->getReferenceArguments(), frameToCopy->getReferenceMetric() );
- // Copy weight
- mymsd->setWeight( frameToCopy->getWeight() );
- // Easy bit - copy the frame
- frames.push_back( mymsd );
- // This resizes the low dim array
- resizeRestOfFrame();
-}
+// void MultiReferenceBase::copyFrame( ReferenceConfiguration* frameToCopy ){
+// // Create a reference configuration of the appropriate type
+// ReferenceConfiguration* mymsd=metricRegister().create<ReferenceConfiguration>( frameToCopy->getName() );
+// // Copy names of arguments and and indexes
+// mymsd->setNamesAndAtomNumbers( frameToCopy->getAbsoluteIndexes(), frameToCopy->getArgumentNames() );
+// // Copy reference positions, reference arguments and reference metric
+// mymsd->setReferenceConfig( frameToCopy->getReferencePositions(), frameToCopy->getReferenceArguments(), frameToCopy->getReferenceMetric() );
+// // Copy weight
+// mymsd->setWeight( frameToCopy->getWeight() );
+// // Easy bit - copy the frame
+// frames.push_back( mymsd );
+// // This resizes the low dim array
+// resizeRestOfFrame();
+// }
void MultiReferenceBase::setWeights( const std::vector<double>& weights ){
plumed_assert( weights.size()==frames.size() );
diff --git a/src/reference/MultiReferenceBase.h b/src/reference/MultiReferenceBase.h
index fddb71530216985fe3edd9fa885ba7b20236f827..0d2827133893b835e0dbd84f2b9f9b686e49ed41 100644
--- a/src/reference/MultiReferenceBase.h
+++ b/src/reference/MultiReferenceBase.h
@@ -66,7 +66,7 @@ public:
/// Return the ith reference frame
ReferenceConfiguration* getFrame( const unsigned& iframe );
/// Copy a reference configuration into the multi reference object
- void copyFrame( ReferenceConfiguration* frameToCopy );
+// void copyFrame( ReferenceConfiguration* frameToCopy );
/// Set the weight of the ith frame
void setWeights( const std::vector<double>& ww );
/// Retrieve the weight of one of the frames
diff --git a/src/reference/ReferenceArguments.cpp b/src/reference/ReferenceArguments.cpp
index 50cb4578693659905651505893b8dfe13802b285..a9bc45727a7841206a2e6e4382335c62826f37bd 100644
--- a/src/reference/ReferenceArguments.cpp
+++ b/src/reference/ReferenceArguments.cpp
@@ -38,8 +38,8 @@ void ReferenceArguments::readArgumentsFromPDB( const PDB& pdb ){
if( !aref ) parseVector( "ARG", arg_names );
else parseVector( "ARG", arg_names, true );
- reference_args.resize( arg_names.size() );
- for(unsigned i=0;i<arg_names.size();++i) parse( arg_names[i], reference_args[i] );
+ reference_args.resize( arg_names.size() ); der_index.resize( arg_names.size() );
+ for(unsigned i=0;i<arg_names.size();++i){ parse( arg_names[i], reference_args[i] ); der_index[i]=i; }
if( hasweights ){
plumed_massert( !hasmetric, "should not have weights if we are using metric");
@@ -62,17 +62,6 @@ void ReferenceArguments::readArgumentsFromPDB( const PDB& pdb ){
}
}
-void ReferenceArguments::setArgumentNames( const std::vector<std::string>& arg_vals ){
- reference_args.resize( arg_vals.size() );
- arg_names.resize( arg_vals.size() );
- der_index.resize( arg_vals.size() );
- for(unsigned i=0;i<arg_vals.size();++i){
- arg_names[i]=arg_vals[i]; der_index[i]=i;
- }
- if( hasmetric ) metric.resize( arg_vals.size(), arg_vals.size() );
- else weights.resize( arg_vals.size() );
-}
-
void ReferenceArguments::setReferenceArguments( const std::vector<double>& arg_vals, const std::vector<double>& sigma ){
plumed_dbg_assert( reference_args.size()==arg_vals.size() );
for(unsigned i=0;i<arg_vals.size();++i) reference_args[i]=arg_vals[i];
@@ -120,9 +109,8 @@ void ReferenceArguments::getArgumentRequests( std::vector<std::string>& argout,
}
}
-void ReferenceArguments::printArguments( OFile& ofile, const std::string& fmt, const bool& isproperty ) const {
- if( isproperty ) ofile.printf("REMARK PROPERTIES=%s", arg_names[0].c_str() );
- else ofile.printf("REMARK ARG=%s", arg_names[0].c_str() );
+void ReferenceArguments::printArguments( OFile& ofile, const std::string& fmt ) const {
+ ofile.printf("REMARK ARG=%s", arg_names[0].c_str() );
for(unsigned i=1;i<arg_names.size();++i) ofile.printf(",%s", arg_names[i].c_str() );
ofile.printf("\n");
ofile.printf("REMARK ");
diff --git a/src/reference/ReferenceArguments.h b/src/reference/ReferenceArguments.h
index d1fc4db14e51c1ca2d2fb9512385b91896342f03..0663aa44bea1cd355ffcf50a754cf5915fc70290 100644
--- a/src/reference/ReferenceArguments.h
+++ b/src/reference/ReferenceArguments.h
@@ -73,14 +73,12 @@ public:
unsigned getNumberOfReferenceArguments() const ;
/// Get the arguments required
void getArgumentRequests( std::vector<std::string>&, bool disable_checks=false );
-/// Set the names of the arguments
- void setArgumentNames( const std::vector<std::string>& arg_vals );
/// Set the positions of the refernce arguments
void setReferenceArguments( const std::vector<double>& arg_vals, const std::vector<double>& sigma );
/// Get the value of the ith reference argument
double getReferenceArgument( const unsigned& i ) const ;
/// Print the arguments out
- void printArguments( OFile& ofile, const std::string& fmt, const bool& isproperty ) const ;
+ void printArguments( OFile& ofile, const std::string& fmt ) const ;
/// Return all the reference arguments
const std::vector<double>& getReferenceArguments();
const std::vector<double>& getReferenceMetric();
diff --git a/src/reference/ReferenceAtoms.cpp b/src/reference/ReferenceAtoms.cpp
index c28dc682e8f07b6cdb25c1a9e18bdc50068761cf..b97f2d4cb4c07b3d8e3435dd2b8756035f0136e4 100644
--- a/src/reference/ReferenceAtoms.cpp
+++ b/src/reference/ReferenceAtoms.cpp
@@ -36,17 +36,7 @@ void ReferenceAtoms::readAtomsFromPDB( const PDB& pdb ){
for(unsigned i=0;i<pdb.size();++i){
indices.push_back( pdb.getAtomNumbers()[i] ); reference_atoms.push_back( pdb.getPositions()[i] );
- align.push_back( pdb.getOccupancy()[i] ); displace.push_back( pdb.getBeta()[i] );
- }
- der_index.resize( reference_atoms.size() );
-}
-
-void ReferenceAtoms::setAtomNumbers( const std::vector<AtomNumber>& numbers ){
- reference_atoms.resize( numbers.size() ); align.resize( numbers.size() );
- displace.resize( numbers.size() ); der_index.resize( numbers.size() );
- indices.resize( numbers.size() );
- for(unsigned i=0;i<numbers.size();++i){
- indices[i]=numbers[i]; der_index[i]=i;
+ align.push_back( pdb.getOccupancy()[i] ); displace.push_back( pdb.getBeta()[i] ); der_index.push_back(i);
}
}
diff --git a/src/reference/ReferenceAtoms.h b/src/reference/ReferenceAtoms.h
index 5e7e0c12e79cef387520c281df99d9c228f678dc..6fc17ced1443c70f57d3b9c5c8315be8488819d3 100644
--- a/src/reference/ReferenceAtoms.h
+++ b/src/reference/ReferenceAtoms.h
@@ -45,6 +45,7 @@ class ReferenceAtoms :
virtual public ReferenceConfiguration
{
friend class SingleDomainRMSD;
+friend class MultiDomainRMSD;
private:
/// This flag tells us if the user has disabled checking of the input in order to
/// do fancy paths with weird inputs
@@ -64,8 +65,6 @@ private:
protected:
/// Read in the atoms from the pdb file
void readAtomsFromPDB( const PDB& );
-/// Add atom indices to list
- void setAtomIndices( const std::vector<AtomNumber>& atomnumbers );
/// Read a list of atoms from the pdb input file
bool parseAtomList( const std::string& , std::vector<unsigned>& );
/// Get the vector of alignment weights
@@ -76,12 +75,6 @@ protected:
Vector getReferencePosition( const unsigned& iatom ) const ;
/// Get the reference positions
const std::vector<Vector> & getReferencePositions() const ;
-/// Add derivatives to iatom th atom in list
-// void addAtomicDerivatives( const unsigned& , const Vector& );
-/// Get the atomic derivatives on the ith atom in the list
-// Vector retrieveAtomicDerivatives( const unsigned& ) const ;
-/// Add derivatives to the viral
-// void addBoxDerivatives( const Tensor& );
/// This does the checks that are always required
void singleDomainRequests( std::vector<AtomNumber>&, bool disable_checks );
public:
@@ -92,8 +85,6 @@ public:
unsigned getAtomIndex( const unsigned& ) const ;
/// Get the atoms required (additional checks are required when we have multiple domains)
virtual void getAtomRequests( std::vector<AtomNumber>&, bool disable_checks=false );
-/// Set the indices of the reference atoms
- void setAtomNumbers( const std::vector<AtomNumber>& numbers );
/// Set the positions of the reference atoms
virtual void setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in )=0;
/// Print the atomic positions
@@ -116,13 +107,12 @@ const std::vector<double> & ReferenceAtoms::getDisplace() const {
inline
unsigned ReferenceAtoms::getNumberOfReferencePositions() const {
- plumed_dbg_assert( der_index.size()==reference_atoms.size() );
- return reference_atoms.size();
+ return der_index.size(); // reference_atoms.size();
}
inline
unsigned ReferenceAtoms::getNumberOfAtoms() const {
- return reference_atoms.size();
+ return der_index.size(); // reference_atoms.size();
}
inline
@@ -143,21 +133,6 @@ const std::vector<Vector> & ReferenceAtoms::getReferencePositions() const {
return reference_atoms;
}
-// inline
-// void ReferenceAtoms::addAtomicDerivatives( const unsigned& iatom, const Vector& der ){
-// atom_ders[ getAtomIndex(iatom) ]+=der;
-// }
-
-// inline
-// Vector ReferenceAtoms::retrieveAtomicDerivatives( const unsigned& iatom ) const {
-// return atom_ders[ getAtomIndex(iatom) ];
-// }
-
-// inline
-// void ReferenceAtoms::addBoxDerivatives( const Tensor& vir ){
-// virialWasSet=true; virial+=vir;
-// }
-
inline
const std::vector<AtomNumber>& ReferenceAtoms::getAbsoluteIndexes(){
return indices;
diff --git a/src/reference/ReferenceConfiguration.cpp b/src/reference/ReferenceConfiguration.cpp
index b20e9b9bc37c04e4649bfeb34c204a9e11124228..8e094999578c2781fe1d640502371084ec4ac366 100644
--- a/src/reference/ReferenceConfiguration.cpp
+++ b/src/reference/ReferenceConfiguration.cpp
@@ -45,8 +45,6 @@ std::string ReferenceConfigurationOptions::getMultiRMSDType() const {
ReferenceConfiguration::ReferenceConfiguration( const ReferenceConfigurationOptions& ro ):
name(ro.tt)
-// arg_ders(0),
-// atom_ders(0)
{
weight=0.0;
}
@@ -66,22 +64,14 @@ void ReferenceConfiguration::set( const PDB& pdb ){
if(ignore!=name) error("mismatch for name");
}
if( !parse("WEIGHT",weight,true) ) weight=1.0;
+ // Read in properties
+ parseVector( "PROPERTIES", property_names, true );
+ property_values.resize( property_names.size() );
+ for(unsigned i=0;i<property_names.size();++i) parse( property_names[i], property_values[i] );
+ // And read in rest of pdb
read( pdb );
}
-// void ReferenceConfiguration::setNumberOfArguments( const unsigned& n ){
-// arg_ders.resize(n); tmparg.resize(n);
-// }
-
-// void ReferenceConfiguration::setNumberOfAtoms( const unsigned& n ){
-// atom_ders.resize(n);
-// }
-
-// bool ReferenceConfiguration::getVirial( Tensor& virout ) const {
-// if(virialWasSet) virout=virial;
-// return virialWasSet;
-// }
-
void ReferenceConfiguration::parseFlag( const std::string&key, bool&t ){
Tools::parseFlag(line,key,t);
}
@@ -90,45 +80,6 @@ void ReferenceConfiguration::error(const std::string& msg){
plumed_merror("error reading reference configuration of type " + name + " : " + msg );
}
-void ReferenceConfiguration::setNamesAndAtomNumbers( const std::vector<AtomNumber>& numbers, const std::vector<std::string>& arg ){
- ReferenceAtoms* atoms=dynamic_cast<ReferenceAtoms*>( this );
- if(!atoms){
- plumed_massert( numbers.size()==0, "expecting no atomic positions");
- //setNumberOfAtoms( 0 );
- } else {
- atoms->setAtomNumbers( numbers );
- // setNumberOfAtoms( numbers.size() );
- }
- // Copy the arguments to the reference
- ReferenceArguments* args=dynamic_cast<ReferenceArguments*>( this );
- if(!args){
- plumed_massert( arg.size()==0, "expecting no arguments");
- // setNumberOfArguments(0);
- } else {
- args->setArgumentNames( arg );
- // setNumberOfArguments( arg.size() );
- }
-}
-
-void ReferenceConfiguration::setReferenceConfig( const std::vector<Vector>& pos, const std::vector<double>& arg, const std::vector<double>& metric ){
-// plumed_dbg_assert( pos.size()==atom_ders.size() && arg.size()==arg_ders.size() );
- // Copy the atomic positions to the reference
- ReferenceAtoms* atoms=dynamic_cast<ReferenceAtoms*>( this );
- if(!atoms){
- plumed_massert( pos.size()==0, "expecting no atomic positions");
- } else {
- std::vector<double> align_in( pos.size(), 1.0 ), displace_in( pos.size(), 1.0 );
- atoms->setReferenceAtoms( pos, align_in, displace_in );
- }
- // Copy the arguments to the reference
- ReferenceArguments* args=dynamic_cast<ReferenceArguments*>( this );
- if(!args){
- plumed_massert( arg.size()==0 && metric.size()==0, "expecting no arguments");
- } else {
- args->setReferenceArguments( arg, metric );
- }
-}
-
void ReferenceConfiguration::checkRead(){
if(!line.empty()){
std::string msg="cannot understand the following words from the input line : ";
@@ -143,31 +94,50 @@ bool ReferenceConfiguration::isDirection() const {
double ReferenceConfiguration::calculate( const std::vector<Vector>& pos, const Pbc& pbc, const std::vector<Value*>& vals,
ReferenceValuePack& myder, const bool& squared ) const {
- // clearDerivatives();
std::vector<double> tmparg( vals.size() );
for(unsigned i=0;i<vals.size();++i) tmparg[i]=vals[i]->get();
return calc( pos, pbc, vals, tmparg, myder, squared );
}
-// void ReferenceConfiguration::copyDerivatives( const ReferenceConfiguration* ref ){
-// plumed_dbg_assert( ref->atom_ders.size()==atom_ders.size() && ref->arg_ders.size()==arg_ders.size() );
-// for(unsigned i=0;i<atom_ders.size();++i) atom_ders[i]=ref->atom_ders[i];
-// for(unsigned i=0;i<arg_ders.size();++i) arg_ders[i]=ref->arg_ders[i];
-// virialWasSet=ref->virialWasSet; virial=ref->virial;
-// }
-
void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const double& time, const double& weight, const double& old_norm ){
ofile.printf("REMARK TIME=%f LOG_WEIGHT=%f OLD_NORM=%f\n",time, weight, old_norm );
- print( lunits, ofile, "%f", false ); // HARD CODED FORMAT HERE AS THIS IS FOR CHECKPOINT FILE
+ print( lunits, ofile, "%f" ); // HARD CODED FORMAT HERE AS THIS IS FOR CHECKPOINT FILE
}
-void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const std::string& fmt, const bool& isproperty ){
+void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const std::string& fmt ){
ReferenceArguments* args=dynamic_cast<ReferenceArguments*>(this);
- if(args) args->printArguments( ofile, fmt, isproperty );
+ if( property_names.size()>0 ){
+ ofile.printf("REMARK PROPERTIES=%s", property_names[0].c_str() );
+ for(unsigned i=1;i<property_names.size();++i) ofile.printf(",%s", property_names[i].c_str() );
+ ofile.printf("\nREMARK "); std::string descr2;
+ if(fmt.find("-")!=std::string::npos){
+ descr2="%s=" + fmt + " ";
+ } else {
+ // This ensures numbers are left justified (i.e. next to the equals sign
+ std::size_t psign=fmt.find("%");
+ plumed_assert( psign!=std::string::npos );
+ descr2="%s=%-" + fmt.substr(psign+1) + " ";
+ }
+ for(unsigned i=0;i<property_names.size();++i) ofile.printf( descr2.c_str(),property_names[i].c_str(), property_values[i] );
+ ofile.printf("\n");
+ }
+ if(args) args->printArguments( ofile, fmt );
ReferenceAtoms* atoms=dynamic_cast<ReferenceAtoms*>(this);
- if( atoms && isproperty ) plumed_merror("a set of atoms is not a list of properties");
if(atoms) atoms->printAtoms( lunits, ofile );
- if( !isproperty ) ofile.printf("END\n");
+ ofile.printf("END\n");
+}
+
+void ReferenceConfiguration::clearAllProperties(){
+ property_names.resize(0); property_values.resize(0);
+}
+
+void ReferenceConfiguration::attachProperty( const std::string& name, const double& val ){
+ bool found=false;
+ for(unsigned i=0;i<property_names.size();++i){
+ if( property_names[i]==name ){ found=false; property_values[i]=val; break; }
+ }
+ plumed_dbg_assert( property_names.size()==property_values.size() );
+ if( !found ){ property_names.push_back( name ); property_values.push_back( val ); }
}
double distance( const Pbc& pbc, const std::vector<Value*> & vals, ReferenceConfiguration* ref1, ReferenceConfiguration* ref2, const bool& squared ){
@@ -185,4 +155,5 @@ double distance( const Pbc& pbc, const std::vector<Value*> & vals, ReferenceConf
return dist1;
}
+
}
diff --git a/src/reference/ReferenceConfiguration.h b/src/reference/ReferenceConfiguration.h
index a94a010df5c1be7b981e8be2bdf78d68f1848bce..0dd4ce0f9e03b0ecfa3f5e44b0054f59ce29f178 100644
--- a/src/reference/ReferenceConfiguration.h
+++ b/src/reference/ReferenceConfiguration.h
@@ -66,8 +66,6 @@ private:
double weight;
/// A vector containing all the remarks from the pdb input
std::vector<std::string> line;
-/// This is used to store the values of arguments
-// std::vector<double> tmparg;
/// These are used to do fake things when we copy frames
std::vector<AtomNumber> fake_atom_numbers;
std::vector<std::string> fake_arg_names;
@@ -75,18 +73,12 @@ private:
std::vector<Vector> fake_refatoms;
std::vector<double> fake_refargs;
std::vector<double> fake_metric;
+/// Property values are basically the projections of points
+ std::vector<std::string> property_names;
+ std::vector<double> property_values;
protected:
-/// Derivatives wrt to the arguments
-// std::vector<double> arg_ders;
-/// The virial contribution has to be stored
-// bool virialWasSet;
-// Tensor virial;
-/// Derivatives wrt to the atoms
-// std::vector<Vector> atom_ders;
/// Crash with an error
void error(const std::string& msg);
-/// Clear the derivatives
-// void clearDerivatives();
public:
ReferenceConfiguration( const ReferenceConfigurationOptions& ro );
/// Destructor
@@ -100,10 +92,6 @@ public:
virtual void getAtomRequests( std::vector<AtomNumber>&, bool disable_checks=false ){}
/// Retrieve the arguments that are required for this guy
virtual void getArgumentRequests( std::vector<std::string>&, bool disable_checks=false ){}
-/// Set the final number of arguments
-// virtual void setNumberOfArguments( const unsigned& );
-/// Set the final number of atoms
-// virtual void setNumberOfAtoms( const unsigned& );
/// Set the reference configuration using a PDB
virtual void set( const PDB& );
/// Do all local business for setting the configuration
@@ -117,14 +105,6 @@ public:
/// Calculate the distance from the reference configuration
virtual double calc( const std::vector<Vector>& pos, const Pbc& pbc, const std::vector<Value*>& vals, const std::vector<double>& args,
ReferenceValuePack& myder, const bool& squared ) const=0;
-// /// Return the derivative wrt to the ith atom
-// Vector getAtomDerivative( const unsigned& ) const ;
-// /// Return the derivative wrt to the ith argument
-// double getArgumentDerivative( const unsigned& ) const ;
-/// Return the derivatives of the distance wrt the cell vectors. This returns false
-/// for everything other than DRMSD as these sort of calculations have to be done
-/// separately when you use RMSD
-// bool getVirial( Tensor& virout ) const ;
/// Parse something from the pdb remarks
template<class T>
bool parse( const std::string&key, T&t, bool ignore_missing=false );
@@ -137,13 +117,9 @@ public:
void checkRead();
/// Copy derivatives from one frame to this frame
void copyDerivatives( const ReferenceConfiguration* );
-/// Set the atom numbers and the argument names
- void setNamesAndAtomNumbers( const std::vector<AtomNumber>& numbers, const std::vector<std::string>& arg );
-/// Set the reference structure (perhaps should also pass the pbc and align and displace )
- void setReferenceConfig( const std::vector<Vector>& pos, const std::vector<double>& arg, const std::vector<double>& metric );
/// Print a pdb file containing the reference configuration
void print( const double& lunits, OFile& ofile, const double& time, const double& weight, const double& old_norm );
- void print( const double& lunits, OFile& ofile, const std::string& fmt, const bool& isproperty );
+ void print( const double& lunits, OFile& ofile, const std::string& fmt );
/// Get one of the referene arguments
virtual double getReferenceArgument( const unsigned& i ) const { plumed_error(); return 0.0; }
/// These are overwritten in ReferenceArguments and ReferenceAtoms but are required here
@@ -163,20 +139,18 @@ public:
bool isDirection() const ;
/// Stuff to setup pca
virtual void setupPCAStorage( ReferenceValuePack& mypack ){ plumed_error(); }
+/// This clears the set of properties that have been attached to the file
+ void clearAllProperties();
+/// Attach a property to this reference configuration
+ void attachProperty( const std::string& name, const double& val );
+/// Get the number of properties that are stored in this object
+ unsigned getNumberOfProperties() const ;
+/// Get the inum th property value
+ double getPropertyValue( const unsigned& inum ) const ;
+/// Get the name of the inum th property value
+ std::string getPropertyName( const unsigned& inum ) const ;
};
-// inline
-// Vector ReferenceConfiguration::getAtomDerivative( const unsigned& ider ) const {
-// plumed_dbg_assert( ider<atom_ders.size() );
-// return atom_ders[ider];
-// }
-
-// inline
-// double ReferenceConfiguration::getArgumentDerivative( const unsigned& ider ) const {
-// plumed_dbg_assert( ider<arg_ders.size() );
-// return arg_ders[ider];
-// }
-
inline
void ReferenceConfiguration::setWeight( const double& ww ){
weight=ww;
@@ -236,7 +210,20 @@ unsigned ReferenceConfiguration::getNumberOfReferenceArguments() const {
return 0;
}
+inline
+unsigned ReferenceConfiguration::getNumberOfProperties() const {
+ return property_values.size();
+}
+inline
+double ReferenceConfiguration::getPropertyValue( const unsigned& inum ) const {
+ plumed_dbg_assert( inum<property_values.size() ); return property_values[inum];
+}
+
+inline
+std::string ReferenceConfiguration::getPropertyName( const unsigned& inum ) const {
+ plumed_dbg_assert( inum<property_names.size() ); return property_names[inum];
+}
}
#endif
diff --git a/src/tools/PDB.cpp b/src/tools/PDB.cpp
index f24146ed8acadeea91d85d9ad335d455c01ba10f..6f75869da49c079daed2c6426bb403578982f5e4 100644
--- a/src/tools/PDB.cpp
+++ b/src/tools/PDB.cpp
@@ -28,6 +28,38 @@ using namespace std;
namespace PLMD{
+void PDB::setAtomNumbers( const std::vector<AtomNumber>& atoms ){
+ positions.resize( atoms.size() ); occupancy.resize( atoms.size() );
+ beta.resize( atoms.size() ); numbers.resize( atoms.size() );
+ for(unsigned i=0;i<atoms.size();++i){ numbers[i]=atoms[i]; beta[i]=1.0; occupancy[i]=1.0; }
+}
+
+void PDB::addArgumentNames( const std::vector<std::string>& argument_names ){
+ std::string newrem = "ARG="+argument_names[0];
+ for(unsigned i=1;i<argument_names.size();++i) newrem+="," + argument_names[i];
+ remark.push_back( newrem );
+ for(unsigned i=0;i<argument_names.size();++i) remark.push_back( argument_names[i] + "=0" );
+}
+
+void PDB::setAtomPositions( const std::vector<Vector>& pos ){
+ plumed_dbg_assert( pos.size()==positions.size() );
+ for(unsigned i=0;i<positions.size();++i) positions[i]=pos[i];
+}
+
+void PDB::setArgumentValue( const std::string& argname, const double& val ){
+ bool replaced=false; std::string num; Tools::convert( val, num );
+ for(unsigned i=0;i<remark.size();++i){
+ if( remark[i].find(argname+"=")!=std::string::npos){
+ remark[i]=argname + "=" + num; replaced=true;
+ }
+ }
+ plumed_assert( replaced );
+}
+
+void PDB::addBlockEnd( const unsigned& end ){
+ block_ends.push_back( end );
+}
+
unsigned PDB::getNumberOfAtomBlocks()const{
return block_ends.size();
}
diff --git a/src/tools/PDB.h b/src/tools/PDB.h
index ef458956042c2ff4ec2a856e89e2222f3d61ef3a..7c242fee93c3fcbc36b69d4adce8490108fc1682 100644
--- a/src/tools/PDB.h
+++ b/src/tools/PDB.h
@@ -98,6 +98,16 @@ public:
/// Return the atom named aname from residue number resnum and chain.
/// Chain=="*" matches any chain and makes it equivalent to getNamedAtomFromResidue.
AtomNumber getNamedAtomFromResidueAndChain( const std::string& aname, const unsigned& resnum, const std::string& chain ) const;
+/// This is used in PLMD::analysis::AnalysisWithDataCollection to add the sizes of the domains for PLMD::MultiRMSD
+ void addBlockEnd( const unsigned& end );
+/// This is used in PLMD::analysis::AnalysisWithDataCollection to add the names of the arguments
+ void addArgumentNames( const std::vector<std::string>& argument_names );
+/// This is used in PLMD::analysis::AnalysisWithDataCollection to add the numbers of the atoms
+ void setAtomNumbers( const std::vector<AtomNumber>& atoms );
+/// This is used in PLMD::analysis::AnalysisWithDataCollection to set the atom positions
+ void setAtomPositions( const std::vector<Vector>& pos );
+/// This is used in PLMD::analysis::AnalysisWithDataCollection to set the argument values
+ void setArgumentValue( const std::string& argname, const double& val );
/// Get the extents of the blocks containing the atoms
const std::vector<unsigned> & getAtomBlockEnds() const ;
/// Get the number of blocks of atoms in the pdb